10 Phylogenetic trees are hypotheses Remember phylogenetic trees are hypotheses about the evolutionary relationships between groups.New evidence can be used to test a tree.
11 How to read a phylogenetic tree Each branch tip represents a taxon (a group of related organisms).Interior nodes (where branches meet) represent common ancestors of the taxa at the ends of the branches.
14 How to read a phylogenetic tree Remember there are multiple different ways to depict relationship s in a phylogenetic tree.Any node in a phylogenetic tree can be rotated without altering the relationships between taxa.
17 How to read a phylogenetic tree We build phylogenetic trees to use to figure out evolutionary relationships between taxa and to identify “natural” groupings among taxa, those that reflect their true evolutionary relationships.A key idea is that natural groupings called clades are monophyletic groups.
18 How to read a phylogenetic tree Clade: a group of taxa that share a common ancestor.Monophyletic group: consists of an ancestor and all of the taxa that are descendants of that ancestor.
19 Taxonomic units legitimate only if they represent a clade Clades are monophyletic groups
21 How to read a phylogenetic tree In the next slides elephants, manatees and hyraxes plus their common ancestor form a monophyletic group.Similarly tapirs, rhinoceroses and horses plus their common ancestor form another monophyletic group.
29 Paraphyletic groupAn example of a paraphyletic group among vertebrates is“fish.”All tetrapods (four-legged animals) are descended from lobe-finned fish ancestors, but are not considered “fish” hence “fish” is a paraphyletic group because the tetrapods are excluded.
30 Some Linnean classifications are not monophyletic
32 Rooted vs. unrooted trees Trees we’ve seen so far have been rooted and these trees give a clear indication of the direction of time.However, computer programs that produce phylogenetic trees often produce unrooted trees.
33 Rooted vs. unrooted trees In an unrooted tree, branch tips are more recent than interior nodes, but you cannot tell which of multiple interior nodes is more recent than others.
37 Rooted vs. unrooted trees There is only one true tree of evolutionary relationships.To identify that tree we must root the tree correctly.Using an outgroup is the easiest way to root a tree.
38 Rooted vs. unrooted trees An outgroup is a close relative of the members of the ingroup (the various species being studied) that provides a basis for comparison with the others.
39 Rooted vs. unrooted trees The outgroup lets us know if a character state within the ingroup is ancestral or not.If the outgroup and some of the ingroup possess a character state then that character state is considered ancestral.
40 Rooted vs. unrooted trees Consider an unrooted tree of four magpie species.
41 Figure 5.15 Phylogeny of magpie populations. (A) The black-billed magpie (Pica hudsonia). (B) An unrooted phylogenetic tree showing relationships among four magpie populations: the Korean magpie (Pica pica sericea), the Eurasian magpie (Pica pica pica), the black-billed magpie (Pica hudsonia), and the yellow-billed magpie (Pica nuttalli). This phylogeny is based on a maximum parsimony phylogeny derived using mitochondrial DNA sequences. Part B adapted from Lee et al. (2003).
42 Rooted vs. unrooted trees To root the tree we need a group that split off earlier from the lineage that led to these four species of magpies.Azure-winged magpie is a suitable outgroup. One this is added to the unrooted tree we can root the tree.
43 Figure 5.16a Rooting the magpie phylogeny using an outgroup. The azure-winged magpie (Cyanopica cyana) serves as an outgroup for the genus Pica. On the unrooted tree (A), the red dot indicates the point around which we will root the tree. The rooted tree (B) has the azure-winged magpie as an outgroup. Adapted from Lee et al. (2003).
44 Figure 5.16b Rooting the magpie phylogeny using an outgroup. The azure-winged magpie (Cyanopica cyana) serves as an outgroup for the genus Pica. On the unrooted tree (A), the red dot indicates the point around which we will root the tree. The rooted tree (B) has the azure-winged magpie as an outgroup. Adapted from Lee et al. (2003).
45 Branch lengths of trees In some phylogenetic trees branches are drawn with different lengths.In these trees branch lengths represent the amount of evolutionary change that has occurred in that lineage.
47 Building a phylogenetic tree--Homologous and analagous traits Homologous traits are derived from a common ancestor.E.g. all mammals possess hair. This is a homologous trait all mammals share because they inherited it from a common ancestor.Analagous traits are shared by different species not because they were inherited from a common ancestor but because they evolved independently.
49 Divergent evolutionDivergent evolution occurs when closely related populations diverge from each other because selection operates differently on them.Such new species will possess many homologous traits in common.
50 Convegent EvolutionAnalagous traits are the result of a process of convergent evolution whereby the same or similar solution to an evolutionary problem is converged upon by different organisms independently of each other.
53 SynapomorphyWhen building a phylogenetic tree we must use characters inherited from ancestors.Such a character found in two or more taxa is referred to as a shared derived character or synapomorphy. Example B on the next slide is a synapomorphy.
55 SynapomorphyIf all shared traits were shared derived traits tree-building would be straightforward.However, many traits are not e.g. analagous traits
56 HomoplasyWe want to avoid including analagous traits when constructing phylogenetic trees because they can mislead us.An analagous trait in a tree is referred to as a homoplasy.
57 Not all traits are similar due to common descent Homoplasy: character state similarity not due to common descentConvergent evolution: independent evolution of similar traitEvolutionary reversals: reversion back to an ancestral character state
58 HomoplasyIn the next slide (A) we do not know the ancestral color state so we have to represent it as unresolved (a polytomy).If we know that our phylogenetic tree (B) correctly indicates the relationships between taxa then we know that dark coloration is a homoplasy having evolved independently twice.
60 SymplesiomorphyAnother way in which we could be mistaken is if a new trait arises in a lineage and is not shared with other taxa. This is called a symplesiomorphy.In the next slide, light coloration has recently arisen in taxon 3. If we thought dark coloration was a shared derived character we would group species 1+2, (as in A) but it isn’t. Instead dark coloration is an ancestral trait and the correct phylogeny is shown in B.
62 Strategies to avoid homoplasies and symplesiomorphies Several strategies exist to limit homoplasies and synapomorphies.1. use traits that change relatively slowly in evolutionary time2. use many traits to build the tree3. use multiple outgroups to help identify ancestral values of traits.
63 Building a phylogeny of Carnivora (Box 4.1 in text) The mammalian order Carnivora includes cats, dogs and other familiar predatory mammals.Certain synapomorphies such as carnassial teeth (enlarged side teeth used to shear meat) unite the group, but there has been debate about relationships within the group.
64 Construction of phylogenies is based on analysis of characters To analyze relationships among 10 species of carnivores we construct a data matrix of the distribution of a dozen traits across these taxa.
66 Clades are determined by synapomorphies Using synapomorphies to identify clades we can construct a phylogentic tree. The numbers on the tree correspond to the character states in the matrix.Some clades in tree are clearly defined but others not so well.
67 One point where relationships are unresolved. Such uncertain branching is called a polytomy.
68 Adding data to the matrix If we add a 13th trait to the data matrix we may be able to resolve the polytomy.However, sometimes additional data doesn’t help or introduces more uncertainty.
70 Absence of a lower premolar is a character shared by cats, hyenas and otters, but that doesn’t fit with our previous tree.Most likely this is a homoplasy (and the tooth was lost independently in different lineages).
72 In reality phylogentic analyses inevitably involved dealing with conflicting evidence. The most commonly applied rule to resolve conflict is the principle of parsimony – choosing the simplest explanation i.e., the phylogeny that requires the fewest trait changes to construct it.
73 Consensus treesApplying the principle of phylogeny to a larger (20 character) matrix of data reveals three equally parsimonious phylogenetic trees that differ somewhat from each other.Notice, however, that certain portions of the tree are consistent across all three trees.Using some mathematical analysis a consensus tree can be constructed that represents a “best estimate” of the true tree.
74 Three equally parsimonious trees (above) Consensus tree (below).
75 Birds are dinosaurs: tracking the evolution of feathers and flight Archaeopteryx, discovered in 1860, dates to 145 mya
76 Traits often change function over time Traits often change function over time. Phylogenies allow us to track such changes over evolutionary time.The oldest known fossil bird is Archaeopteryx (145mya), which possesses a suite of both avian and reptilian characteristics.
77 Birds today are defined by the possession of feathers and obviously they are used to fly, but phylogenetic analysis shows that this was not the original function of feathers as feathers are present in non-flying ancestral groups.Phylogenetic analysis also reveals that birds evolved from dinosaurs.
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